title: Genotype impact on HCV RNA levels determined with the VERSANT HCV RNA 1.0 assay (kPCR).
abstract: BACKGROUND
  Accurate quantitation of hepatitis C virus (HCV) RNA is mandatory for the management of anti-HCV therapy.
  
  
  OBJECTIVE
  The genotype-dependent performance of the new commercially available VERSANT HCV RNA 1.0 Assay (kPCR) and the COBAS AmpliPrep/COBAS TaqMan HCV Quantitative Test, version 2.0 was investigated.
  
  
  METHODS
  The molecular assays for quantitation of HCV RNA were performed according to the manufacturer's package insert instructions. HCV genotypes/subtypes/isolates, and mutations in the 5'NCR were detected by direct sequencing.
  
  
  RESULTS
  When members of a worldwide HCV performance panel including HCV subtypes 1a, 1b, 2a, 3b, and 4a were tested with the Siemens assay and the results were compared with those obtained by the Roche assay, the mean log10 unit differences for members containing HCV subtypes 1a, 1b, 3b, and 4a were found to be within ±0.5 log(10) units. For the panel member containing HCV subtype 2a, the HCV RNA concentration was found to be >0.5 log(10) units lower with the Siemens assay. When clinical samples were tested, the HCV RNA concentration of all samples containing HCV subtype 2a were found to be >0.5 log(10) units lower with the Siemens assay while that of certain HCV subtype 3a and 4a isolates were found to be >1.0 log(10) units lower.
  
  
  CONCLUSIONS
  The VERSANT HCV RNA 1.0 Assay substantially underestimates HCV RNA concentrations in HCV subtype 2a samples and in HCV subtype 3a and 4a samples containing certain isolates. This may be caused by mismatches with the target sequences due to the primer and/or probe design.
authors.affiliation: Research Unit Molecular Diagnostics and Molecular Diagnostics Laboratory, IHMEM, Medical University of Graz, Graz, Austria. Electronic address: harald.kessler@medunigraz.at.
authors.forename: Harald H
authors.initials: HH
authors.lastname: Kessler
authors.forename: Margit
authors.initials: M
authors.lastname: Hübner
authors.forename: Petra M
authors.initials: PM
authors.lastname: Konrad
authors.forename: Evelyn
authors.initials: E
authors.lastname: Stelzl
authors.forename: Madeleine M
authors.initials: MM
authors.lastname: Stübler
authors.forename: Merve H
authors.initials: MH
authors.lastname: Baser
authors.forename: Brigitte I
authors.initials: BI
authors.lastname: Santner
mesh_terms: D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D019562:Viral Load / Q000379:methods*
chemical_list: D012367:RNA, Viral
keywords: COBAS TaqMan HCV; Genotype; Quantitation; Real-time PCR; Subtype; Versant HCV RNA